A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential \(^{1}\hbox {H}\) data acquisition for moderately sized proteins is presented. The suitability of the approach for obtaining sequential resonance assignments, including complete \(^{15}\hbox {N}{},\, ^{1}\hbox {H}{}^{N},\, ^{13}\hbox {CO}{},\, ^{13}\hbox {C}^{\alpha }{},\, ^{13}\hbox {C}^{\beta }\) and \(^{1}\hbox {H}^{\alpha }\) chemical shift information, is demonstrated experimentally for a \(^{13}\hbox {C}\) and \(^{15}\hbox {N}\) labelled sample of the C-terminal winged helix (WH) domain of the minichromosome maintenance (MCM) complex of Sulfolobus solfataricus. The chemical shift information obtained was used to calculate the global fold of this winged helix domain via CS-Rosetta. This demonstrates that our procedure provides a reliable and straight-forward protocol for a quick global fold determination of moderately-sized proteins.
[NMR paper] NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction.
NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction.
Related Articles NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction.
BMC Bioinformatics. 2013 Mar 16;14(1):98
Authors: Dehof AK, Loew S, Lenhof HP, Hildebrandt A
Abstract
NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking...
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03-19-2013 01:22 PM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction...
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12-01-2012 06:10 PM
Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins
Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
Yi-Jan Lin, Donata K. Kirchner, Peter Güntert</br>
Homodimeric proteins pose a difficulty for NMR structure determination because the degeneracy of the chemical shifts in the two identical monomers implies an ambiguity in all assignments of distance restraints. For homodimeric proteins, residues involved in the interface between two monomers provide essential intermolecular NOEs. The...
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07-14-2012 01:53 PM
4D Non-uniformly sampled HCBCACON and 1J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins
4D Non-uniformly sampled HCBCACON and 1J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins
Abstract A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit 13C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (Hα, and Hβ) and carbon (Cα, Cβ) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient...
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05-17-2012 08:40 AM
Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
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07-15-2011 09:10 PM
[NMR paper] CAMRA: chemical shift based computer aided protein NMR assignments.
CAMRA: chemical shift based computer aided protein NMR assignments.
Related Articles CAMRA: chemical shift based computer aided protein NMR assignments.
J Biomol NMR. 1998 Oct;12(3):395-405
Authors: Gronwald W, Willard L, Jellard T, Boyko RF, Rajarathnam K, Wishart DS, Sönnichsen FD, Sykes BD
A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORB, CAPTURE and PROCESS. ORB predicts NMR chemical shifts...
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11-17-2010 11:15 PM
Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data.
Related Articles Protein secondary structure prediction using NMR chemical shift data.
J Bioinform Comput Biol. 2010 Oct;8(5):867-84
Authors: Zhao Y, Alipanahi B, Li SC, Li M
Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...
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10-29-2010 07:05 PM
A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
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